RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780474|ref|YP_003064887.1| ubiquinol oxidase, subunit II
[Candidatus Liberibacter asiaticus str. psy62]
(332 letters)
>1fft_B Ubiquinol oxidase; electron transport, cytochrome oxidase, membrane
protein, oxidoreductase; HET: HEM HEO; 3.50A
{Escherichia coli} SCOP: b.6.1.2 f.17.2.1
Length = 315
Score = 296 bits (759), Expect = 5e-81
Identities = 132/309 (42%), Positives = 189/309 (61%), Gaps = 11/309 (3%)
Query: 14 KSLKFFFLFFSSVMLSGFEFIVMDPYGDIALQQASLIRIAVALMLLIVVPVFFSILFFAW 73
KSL + LF +V+LSG ++DP G I L+Q SLI A LML++V+P + FAW
Sbjct: 8 KSLGWLSLFAGTVLLSGCNSALLDPKGQIGLEQRSLILTAFGLMLIVVIPAILMAVGFAW 67
Query: 74 KYRSTNKKARYDPKWCHSTLLELFVWLVPLVIVGFLAVITWDATHRMDPYAPLERISESK 133
KYR++NK A+Y P W HS +E VW VP++I+ FLAV+TW TH ++P PL
Sbjct: 68 KYRASNKDAKYSPNWSHSNKVEAVVWTVPILIIIFLAVLTWKTTHALEPSKPL------- 120
Query: 134 SIAKNSKPLVVEVVALDWKWLFLLPEQQVAIINELVVPIDRPLEFRITASSVMNSFYIPG 193
A + KP+ +EVV++DWKW F+ PEQ +A +NE+ P + P+ F++T++SVMNSF+IP
Sbjct: 121 --AHDEKPITIEVVSMDWKWFFIYPEQGIATVNEIAFPANTPVYFKVTSNSVMNSFFIPR 178
Query: 194 LAGQIYAMAGMETKLHAVMNKKGAYSGFSANYSGRGFSHMRFKFYGKS-EKGFEDWISKV 252
L QIYAMAGM+T+LH + N+ G Y G SA+YSG GFS M+FK F+ W++K
Sbjct: 179 LGSQIYAMAGMQTRLHLIANEPGTYDGISASYSGPGFSGMKFKAIATPDRAAFDQWVAKA 238
Query: 253 KRQG-TFLNRQEYLLLKKPSERDSVRYFSPIEKGLYYSILNLCVHPGKICMDEMMRIDAL 311
K+ T + + L PSE + V YFS ++ L+ ++N + GK +
Sbjct: 239 KQSPNTMSDMAAFEKLAAPSEYNQVEYFSNVKPDLFADVINKFMAHGKSMDMTQPEGEHS 298
Query: 312 GGGGMRGID 320
GM G+D
Sbjct: 299 AHEGMEGMD 307
>1cyx_A CYOA; electron transport; 2.30A {Escherichia coli} SCOP: b.6.1.2
PDB: 1cyw_A
Length = 205
Score = 165 bits (419), Expect = 1e-41
Identities = 76/206 (36%), Positives = 115/206 (55%), Gaps = 11/206 (5%)
Query: 117 THRMDPYAPLERISESKSIAKNSKPLVVEVVALDWKWLFLLPEQQVAIINELVVPIDRPL 176
TH ++P PL + KP+ +EVV++DWKW F+ PEQ +A +NE+ P + P+
Sbjct: 1 THALEPSKPLAH---------DEKPITIEVVSMDWKWFFIYPEQGIATVNEIAFPANTPV 51
Query: 177 EFRITASSVMNSFYIPGLAGQIYAMAGMETKLHAVMNKKGAYSGFSANYSGRGFSHMRFK 236
F++T++SVM+SF+IP L QIYAMAGM+T+LH + N+ G Y G A G G S M+FK
Sbjct: 52 YFKVTSNSVMHSFFIPRLGSQIYAMAGMQTRLHLIANEPGTYDGICAEICGPGHSGMKFK 111
Query: 237 FYG-KSEKGFEDWISKVKRQG-TFLNRQEYLLLKKPSERDSVRYFSPIEKGLYYSILNLC 294
F+ W++K K+ T + + L PSE + V YFS ++ L+ ++N
Sbjct: 112 AIATPDRAAFDQWVAKAKQSPNTMSDMAAFEKLAAPSEYNQVEYFSNVKPDLFADVINKF 171
Query: 295 VHPGKICMDEMMRIDALGGGGMRGID 320
+ GK + GM G+D
Sbjct: 172 MAHGKSMDMTQPEGEHSAHEGMEGMD 197
>3hb3_B Cytochrome C oxidase subunit 2; electron transfer, proton transfer,
proton pumping, membrane protein, cell inner membrane,
cell membrane, copper; HET: HEA LDA LMT; 2.25A
{Paracoccus denitrificans} PDB: 1ar1_B* 3ehb_B* 1qle_B*
Length = 298
Score = 123 bits (309), Expect = 6e-29
Identities = 42/241 (17%), Positives = 93/241 (38%), Gaps = 39/241 (16%)
Query: 37 DPYGDIALQQASLIRIAVALMLLIVVPVFFSILFFAWKYRSTNKKARYDPKWCHSTLLEL 96
+A Q L + ++ + + V +L ++ + ++ H+T +E+
Sbjct: 51 PASSPLAHDQQWLDHFVLYIITAVTIFVCLLLLICIVRFN--RRANPVPARFTHNTPIEV 108
Query: 97 FVWLVPLVIVGFLAVITWDATHRMDPYAPLERISESKSIAKNSKPLVVEVVALDWKWLF- 155
LVP++I+ + + R N LV++ + W W +
Sbjct: 109 IWTLVPVLILVAIGAFSLPILFRSQEM-------------PNDPDLVIKAIGHQWYWSYE 155
Query: 156 -----------------------LLPEQQVAIINELVVPIDRPLEFRITASSVMNSFYIP 192
E +A N +VVP+ + + ++TA+ V++++ IP
Sbjct: 156 YPNDGVAFDALMLEKEALADAGYSEDEYLLATDNPVVVPVGKKVLVQVTATDVIHAWTIP 215
Query: 193 GLAGQIYAMAGMETKLHAVMNKKGAYSGFSANYSGRGFSHMRFKFYGKSEKGFEDWISKV 252
A + A+ G +L ++++G Y G + G ++M S++ +E W++
Sbjct: 216 AFAVKQDAVPGRIAQLWFSVDQEGVYFGQCSELCGINHAYMPIVVKAVSQEKYEAWLAGA 275
Query: 253 K 253
K
Sbjct: 276 K 276
>2gsm_B Cytochrome C oxidase subunit 2; transmembrane protein complex,
oxidoreductase; HET: DMU HEA TRD; 2.00A {Rhodobacter
sphaeroides} SCOP: b.6.1.2 f.17.2.1 PDB: 3dtu_B* 3fye_B*
3fyi_B* 1m56_B* 1m57_B*
Length = 262
Score = 104 bits (260), Expect = 3e-23
Identities = 41/237 (17%), Positives = 85/237 (35%), Gaps = 22/237 (9%)
Query: 37 DPYGDIALQQASLIRIAVALMLLIVVPVFFSILFFAWKYR-STNKKARYDPKWCHSTLLE 95
+A Q L + ++ I + V IL+ W++ NK +
Sbjct: 20 PSASPVATQIHWLDGFILVIIAAITIFVTLLILYAVWRFHEKRNKVPARFTHNSPLEIAW 79
Query: 96 LFVWLVPLVIVGFLAVITWDATHRMDP-----------------YAPLERISESKSIAKN 138
V +V LV +G ++ + Y E ES I
Sbjct: 80 TIVPIVILVAIGAFSLPVLFNQQEIPEADVTVKVTGYQWYWGYEYPDEEISFESYMIGSP 139
Query: 139 S----KPLVVEVVALDWKWLFLLPEQQVAIINELVVPIDRPLEFRITASSVMNSFYIPGL 194
+ + EV + + E +A +VVP+++ + ++T + V++S+ +P
Sbjct: 140 ATGGDNRMSPEVEQQLIEAGYSRDEFLLATDTAMVVPVNKTVVVQVTGADVIHSWTVPAF 199
Query: 195 AGQIYAMAGMETKLHAVMNKKGAYSGFSANYSGRGFSHMRFKFYGKSEKGFEDWISK 251
+ A+ G +L ++G + G + G ++M SE+ + W+ +
Sbjct: 200 GVKQDAVPGRLAQLWFRAEREGIFFGQCSELCGISHAYMPITVKVVSEEAYAAWLEQ 256
>1v54_B Cytochrome C oxidase polypeptide II; oxidoreductase; HET: FME TPO
HEA TGL PGV CHD CDL PEK PSC DMU; 1.80A {Bos taurus}
SCOP: b.6.1.2 f.17.2.1 PDB: 1oco_B* 1occ_B* 1ocz_B*
1ocr_B* 1v55_B* 2dyr_B* 2dys_B* 2eij_B* 2eik_B* 2eil_B*
2eim_B* 2ein_B* 2occ_B* 2zxw_B*
Length = 227
Score = 89.6 bits (222), Expect = 8e-19
Identities = 35/217 (16%), Positives = 74/217 (34%), Gaps = 42/217 (19%)
Query: 56 LMLLIVVPVFFSILFFAWKYRSTNKKARYDPKWCHSTLLELFVWLVPLVIVGFLAVITWD 115
++ LI V + I + +E ++P +I+ +A+ +
Sbjct: 30 IVFLISSLVLYIISLMLTTKL-------THTSTMDAQEVETIWTILPAIILILIALPSLR 82
Query: 116 ATHRMDPYAPLERISESKSIAKNSKPLVVEVVALDWKW---------------------L 154
+ MD N+ L V+ + W W L
Sbjct: 83 ILYMMDEI--------------NNPSLTVKTMGHQWYWSYEYTDYEDLSFDSYMIPTSEL 128
Query: 155 FLLPEQQVAIINELVVPIDRPLEFRITASSVMNSFYIPGLAGQIYAMAGMETKLHAVMNK 214
+ + + N +V+P++ + +++ V++S+ +P L + A+ G + + ++
Sbjct: 129 KPGELRLLEVDNRVVLPMEMTIRMLVSSEDVLHSWAVPSLGLKTDAIPGRLNQTTLMSSR 188
Query: 215 KGAYSGFSANYSGRGFSHMRFKFYGKSEKGFEDWISK 251
G Y G + G S M K FE W +
Sbjct: 189 PGLYYGQCSEICGSNHSFMPIVLELVPLKYFEKWSAS 225
>1xme_B Cytochrome C oxidase polypeptide II; cytochrome oxidase, heme,
heme-AS, integral membrane protein, oxidoreductase; HET:
BNG HEM HAS; 2.30A {Thermus thermophilus} SCOP: b.6.1.2
f.17.2.1 PDB: 1ehk_B* 2qpd_B* 2qpe_B* 3bvd_B* 3eh5_B*
3eh3_B* 3eh4_B*
Length = 168
Score = 84.0 bits (207), Expect = 4e-17
Identities = 25/179 (13%), Positives = 58/179 (32%), Gaps = 31/179 (17%)
Query: 74 KYRSTNKKARYDPKWCHSTLLELFVWLVPLVIVGFLAVITWDATHRMDPYAPLERI---- 129
++++ Y+ W + ++ F+A+I + P ++
Sbjct: 4 EHKAHKAILAYEKGW---------LAFSLAMLFVFIALIAYTLATHTAGVIPAGKLERVD 54
Query: 130 ----------SESKSIAKNSKPLVVEVVALDWKWLFLLPEQQVAIINELVVPIDRPLEFR 179
++ + P V L + + + N + VP + F+
Sbjct: 55 PTTVRQEGPWADPAQAVVQTGPNQYTVYVLAFAFGYQP--------NPIEVPQGAEIVFK 106
Query: 180 ITASSVMNSFYIPGLAGQIYAMAGMETKLHAVMNKKGAYSGFSANYSGRGFSHMRFKFY 238
IT+ V++ F++ G + + G + + + G Y Y G G +M
Sbjct: 107 ITSPDVIHGFHVEGTNINVEVLPGEVSTVRYTFKRPGEYRIICNQYCGLGHQNMFGTIV 165
>2cua_A Protein (CUA); CUA center, electron transport; 1.60A {Thermus
thermophilus} SCOP: b.6.1.2 PDB: 2fwl_B*
Length = 135
Score = 70.5 bits (172), Expect = 5e-13
Identities = 26/134 (19%), Positives = 48/134 (35%), Gaps = 21/134 (15%)
Query: 116 ATHR--MDPYAPLERI-----------SESKSIAKNSKPLVVEVVALDWKWLFLLPEQQV 162
ATH + P LER+ ++ + P V L + + +
Sbjct: 5 ATHTAGVIPAGKLERVDPTTVRQEGPWADPAQAVVQTGPNQYTVYVLAFAFGY------- 57
Query: 163 AIINELVVPIDRPLEFRITASSVMNSFYIPGLAGQIYAMAGMETKLHAVMNKKGAYSGFS 222
N + VP + F+IT+ V++ F++ G + + G + + + G Y
Sbjct: 58 -QPNPIEVPQGAEIVFKITSPDVIHGFHVEGTNINVEVLPGEVSTVRYTFKRPGEYRIIC 116
Query: 223 ANYSGRGFSHMRFK 236
Y G G +M
Sbjct: 117 NQYCGLGHQNMFGT 130
>1oqw_A Fimbrial protein; type IV pilin, fiber-forming protein, adhesion,
pseudomonas aerugionosa, PAK pilin, cell adhesion; 2.00A
{Pseudomonas aeruginosa} SCOP: d.24.1.1
Length = 144
Score = 30.2 bits (67), Expect = 0.64
Identities = 14/62 (22%), Positives = 23/62 (37%), Gaps = 7/62 (11%)
Query: 92 TLLELFVWLVPLVIVGFLAVITWDATHRMDPYAPLERISESKSIAKNSKPLVVEVVALDW 151
TL+EL ++ + I+G LA I A + Y + + + K VE
Sbjct: 2 TLIEL---MIVVAIIGILAAI---AIPQYQNYVARSEGASALASVNPLK-TTVEEALSRG 54
Query: 152 KW 153
Sbjct: 55 WS 56
>1kzy_C Tumor suppressor P53-binding protein 1; tandem-BRCT and linker
complexed with non-BRCT protein, three-helix bundle,
parallel beta sheet; 2.50A {Homo sapiens} SCOP: c.15.1.4
c.15.1.4 PDB: 1gzh_B
Length = 259
Score = 27.4 bits (60), Expect = 4.4
Identities = 11/70 (15%), Positives = 21/70 (30%), Gaps = 1/70 (1%)
Query: 246 EDWISKVKRQGTFLNRQEYLLLKKPSERDSVRYFSPIEKGLYYSILNLCVHPG-KICMDE 304
W+ N + YLL S + + + ++ L V + ++
Sbjct: 115 HVWVHDSCHANQLQNYRNYLLPAGYSLEEQRILDWQPRENPFQNLKVLLVSDQQQNFLEL 174
Query: 305 MMRIDALGGG 314
I GG
Sbjct: 175 WSEILMTGGA 184
>1oxw_A Patatin; alpha/beta class fold with approximately three layers;
2.20A {Solanum cardiophyllum} SCOP: c.19.1.3
Length = 373
Score = 26.8 bits (58), Expect = 7.2
Identities = 8/18 (44%), Positives = 14/18 (77%)
Query: 302 MDEMMRIDALGGGGMRGI 319
+ EM+ + ++ GGG+RGI
Sbjct: 12 LGEMVTVLSIDGGGIRGI 29
Database: pdb70
Posted date: Jan 26, 2011 11:21 AM
Number of letters in database: 5,693,230
Number of sequences in database: 24,244
Lambda K H
0.326 0.141 0.437
Gapped
Lambda K H
0.267 0.0486 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 3,010,336
Number of extensions: 138639
Number of successful extensions: 433
Number of sequences better than 10.0: 1
Number of HSP's gapped: 422
Number of HSP's successfully gapped: 27
Length of query: 332
Length of database: 5,693,230
Length adjustment: 93
Effective length of query: 239
Effective length of database: 3,438,538
Effective search space: 821810582
Effective search space used: 821810582
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 57 (26.3 bits)